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bioconductor-visiumstitched

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Enable downstream analysis of Visium capture areas stitched together with Fiji

Installation

To install this package, run one of the following:

Conda
$conda install bioconda::bioconductor-visiumstitched

Usage Tracking

1.2.0
1 / 8 versions selected
Downloads (Last 6 months): 0

Description

This package provides helper functions for working with multiple Visium capture areas that overlap each other. This package was developed along with the companion example use case data available from https://github.com/LieberInstitute/visiumStitched_brain. visiumStitched prepares SpaceRanger (10x Genomics) output files so you can stitch the images from groups of capture areas together with Fiji. Then visiumStitched builds a SpatialExperiment object with the stitched data and makes an artificial hexagonal grid enabling the seamless use of spatial clustering methods that rely on such grid to identify neighboring spots, such as PRECAST and BayesSpace. The SpatialExperiment objects created by visiumStitched are compatible with spatialLIBD, which can be used to build interactive websites for stitched SpatialExperiment objects. visiumStitched also enables casting SpatialExperiment objects as Seurat objects.

About

Summary

Enable downstream analysis of Visium capture areas stitched together with Fiji

Last Updated

Mar 3, 2026 at 08:08

License

Artistic-2.0

Supported Platforms

noarch